The Burrup Peninsula in north-west Western Australia is home to one of the most substantial collections of rock engravings, or petroglyphs, in the world. These petroglyphs are carved through the dark coloured patina, commonly referred to as rock varnish, into the weathering rind of the local parent rock. Rock varnish is essentially a thin layer of manganese (Mn) and iron (Fe) oxides and hydroxides with embedded clay minerals, the formation of which is relatively poorly understood. It is generally considered to be a hostile environment for microorganisms due to extreme environmental conditions including low nutrient availability, lack of water, exposure to extreme ultraviolet radiation and intense seasonal and diurnal temperature fluctuations. However, despite these environmental extremes, microorganisms have been found on and in rock varnish and have been reported as playing a significant role in the formation of rock varnish. Given this, it is likely that any change in local environmental conditions will influence the types and activities of microorganisms found in and on rock varnish and associated rock art. This article focuses on the major influences on the microbiome of culturally important rock art in the Burrup Peninsula and the implications of any environmental change on the rock art itself.